I am experiencing a very similar problem on JOSM. I download something from the server then make a coupe changes then try to re upload and it says I have version 2 and the object is now on version 4. I update data but it does not detect a mismatch. none of this makes sense, as I literally just downloaded from the server one or 2 minutes before. I was heavily editing one area, and it appears that the data i am downloading from uploading to the server is not matching what i am downloading from the server a immediately after.